This is a good question.<br><br>> You can perform fiber tracking in the native MRI space. Here "native" means the MRI data as they were acquired.<br>> You can also perform fiber tracking after you standardized the MRI data in the standard coordinate.<br>
>> The standardization is either by linear or non-linear transformation. For the linear, you can use rigid (just relocate the brain to a standard position and orientation without changing the shape) or affine (you can adjust the brain size and shape too).<br>
>> To perform fiber tracking after the standardization, you have to standardize the tensor file, not FA or vector file. You'd better standardize the tensor file, then create new FA and vector maps from the standardized tensor because standardization of a vector field is difficult.<br>
>> After standardization, you can expect ROI drawing could be more reproducible. For example, if you want to identify the anterior limb of internal capsule for fiber tracking, you can create a protocol like, "draw ROI on the internal capsule at coronal slice #50". This kind of protocol is not applicable if we use the native space.<br>
>> Also, standardization often involves interpolation to finer resolution (say 2.5 mm native resolution to 1 mm standard coordinates). This has some impact on fiber tracking. I believe the fiber-angle threshold (this prevents sharp turning angle) is effectively reduced. So, you may obtain longer uninterrupted streamlines. Cosmetically, the tracking results may look better with finer resolution.<br>
>> Drawback is, because of the extra standardization step that involves interpolation, blurring, tensor re-orientation, and other issues, you may invite some questions and criticisms.<br><br>In my personal opinion, it is not an issue of one is better than the other. You need to decide the way you do the study and stick to it. I personally support the standardized approach.<br>
<br>Susumu<br><br><div class="gmail_quote">2010/1/17 yan hao <span dir="ltr"><<a href="mailto:hao_y@hsc.pku.edu.cn" target="_blank">hao_y@hsc.pku.edu.cn</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all,<br>
I wonder if I need to do spatial normalization before I do the fiber tracking. I know I can do this in the original space. However some fibers are not easy to define in the original space, so if the images are all in a standard space, I can draw a ROI in a certain slice of the brain.If the spatial normalization is acceptable, could you suggest the way to do the spatial normalization£¿Any help is highly appreciated.<br>
Best,Hao_______________________________________________Mristudio-users mailing listMristudio-users@mristudio.orghttp://<a href="http://lists.mristudio.org/mailman/listinfo/Unsubscribe" target="_blank">lists.mristudio.org/mailman/listinfo/Unsubscribe</a>, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
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